SiOx thin films with different stoichiometry degree were obtained by plasma-enhanced chemical vapor deposition on crystalline silicon substrates from SiH4 and N2O gas mixtures. Two twin sets of samples were irradiated by 380 keV Ar+ ions at a fluence of 5×1016 ions/cm2 at room temperature and at 500 °C, respectively, and then annealed in vacuum at different temperatures, between 500 and 1100 °C. A set of unirradiated samples has been annealed in the same conditions in order to discriminate the contribution of ion irradiation and of thermal treatments to the changes of the film microstructure. The structural modification of the oxide network and the growth of Si nanoclusters have been studied by vibrational spectroscopy techniques. Fourier transform infrared absorption spectra evidenced that ion irradiation induces a hydrogen loss of about 50%, and that postirradiation thermal treatments lead to the recovery of the irradiation defects and to the out diffusion of the residual hydrogen. After heating at 800 °C, irradiated and unirradiated samples exhibit substantially the same structure from the point of view of infrared-absorption spectra. In the meanwhile, the Si-O-Si stretching peak blue shifts, but never reaches the wavenumber value of pure silica owing to the presence of nitrogen into the network. Raman spectra of as-irradiated films reveal the presence of an amorphous silicon phase within the damaged layer of the oxide matrix. Raman spectra of irradiated samples undergoing thermal treatments at high temperature indicate a rearrangement of the film microstructure with the progressive clustering of the amorphous silicon phase. However, no clear spectroscopic evidence is gained about the crystallization of silicon nanoclusters, even after annealing at the highest temperature. In fact, the Raman scattering from silicon nanocrystals is partially hidden by the Raman peak of the c-Si substrate.